umi_fgbio

This UMI pipeline is based on Fulcrum Genomics toolkit, processes sequencing reads with molecular barcodes (also known as Unique Molecular Indices, UMIs), which provide impressive error correction and increased accuracy using a sequencing consensus read level.

--in-fq [IN_FQ [IN_FQ ...]]

Path to one or more fastq files, each corresponding to a sub-read. Files can be in fastq or fastq.gz format. (default: None)

Option is required.

--ref REF

Path to the reference file (default: None)

Option is required.

--metadata METADATA

Path to a file containing the metadata about the samples. If no file is provided, output reads will be put into unmatched files only. (default: None)

--out-dir OUT_DIR

Path to the directory that will contain all of the generated files. (default: None)

Option is required.

--umi-in-header

Specifies that UMIs are in the read header. (default: False)

-L INTERVAL, --interval INTERVAL

Interval within which to call bqsr from the input reads. All intervals will have a padding of 100 to get read records, and overlapping intervals will be combined. Interval files should be passed using the --interval-file option. This option can be used multiple times (e.g. "-L chr1 -L chr2:10000 -L chr3:20000+ -L chr4:10000-20000") (default: None)

--bwa-options BWA_OPTIONS

Pass supported bwa mem options as one string. The current original bwa mem supported options are -M, -Y, -T (e.g. --bwa-options="-M -Y") (default: None)

--no-warnings

Suppress warning messages about system thread and memory usage. (default: None)

--read-group-sm READ_GROUP_SM

SM tag for read groups in this run. (default: None)

--read-group-lb READ_GROUP_LB

LB tag for read groups in this run. (default: None)

--read-group-pl READ_GROUP_PL

PL tag for read groups in this run. (default: None)

--read-group-id-prefix READ_GROUP_ID_PREFIX

Prefix for the ID and PU tags for read groups in this run. This prefix will be used for all pairs of fastq files in this run. The ID and PU tags will consist of this prefix, and an identifier that will be unique for a pair of fastq files. (default: None)

-ip INTERVAL_PADDING, --interval-padding INTERVAL_PADDING

Amount of padding (in base pairs) to add to each interval you are including. (default: None)

--read-structures [READ_STRUCTURES [READ_STRUCTURES ...]]

The read structure for each of the FASTQs. There must be one read structure per input fastq file. (default: None)

--no-barcode

Remove the requirement that input read structures must contain sample barcodes. (default: None)

--out-metrics OUT_METRICS

The file to which per-barcode metrics are written in the output directory. If none given, a file named demux_barcode_metrics.txt will be written to the output directory. If UMIs are in read header, no metrics file will be generated. (default: None)

--num-zip-threads NUM_ZIP_THREADS

Number of CPUs to use for zipping BAM files in a run (default 16 for coordinate sorts and 10 otherwise). (default: None)

--num-sort-threads NUM_SORT_THREADS

Number of CPUs to use for sorting in a run (default 10 for coordinate sorts and 16 otherwise). (default: None)

--max-records-in-ram MAX_RECORDS_IN_RAM

Maximum number of records in RAM when using a queryname or template coordinate sort mode; lowering this number will decrease maximum memory usage. (default: 65000000)

--strategy STRATEGY

The UMI assignment strategy, which can be adjacency or paired. (default: )

Option is required.

--min-map-q MIN_MAP_Q

Minimum mapping quality. (default: 30)

--num-worker-threads NUM_WORKER_THREADS

Number of threads for worker. (default: 14)

--error-rate-pre-umi ERROR_RATE_PRE_UMI

The Phred-scaled error rate for an error prior to the UMIs being integrated. (default: 45)

--error-rate-post-umi ERROR_RATE_POST_UMI

The Phred-scaled error rate for an error post the UMIs have been integrated. (default: 40)

--min-input-base-quality MIN_INPUT_BASE_QUALITY

Ignore bases in raw reads that have Q below this value. (default: 10)

--min-consensus-base-quality MIN_CONSENSUS_BASE_QUALITY

Mask (make ‘N’) consensus bases with quality less than this threshold. (default: 2)

--min-reads MIN_READS

The minimum number of reads to produce a consensus base. (default: 1)

--out-suffixF OUT_SUFFIXF

Output suffix used for paired reads that are first in pair. The suffix must end with ".gz" (default: _1.fastq.gz)

--out-suffixF2 OUT_SUFFIXF2

Output suffix used for paired reads that are second in pair. The suffix must end with ".gz" (default: _2.fastq.gz)

--out-suffixO OUT_SUFFIXO

Output suffix used for orphan/unmatched reads that are first in pair. The suffix must end with ".gz". If no suffix is provided, these reads will be ignored (default: None)

--out-suffixO2 OUT_SUFFIXO2

Output suffix used for orphan/unmatched reads that are second in pair. The suffix must end with ".gz". If no suffix is provided, these reads will be ignored (default: None)

--out-suffixS OUT_SUFFIXS

Output suffix used for single-end/unpaired reads. The suffix must end with ".gz". If no suffix is provided, these reads will be ignored (default: None)

--rg-tag RG_TAG

Split reads into different fastq files based on the read group tag. Must be either PU or ID (default: None)

--remove-qc-failure

Remove reads from the output that have abstract QC failure. (default: None)

--num-threads NUM_THREADS

Number of threads to run. (default: 8)

--logfile LOGFILE

Path to the log file. If not specified, messages will only be written to the standard error output. (default: None)

--tmp-dir TMP_DIR

Full path to the directory where temporary files will be stored.

--with-petagene-dir WITH_PETAGENE_DIR

Full path to the PetaGene installation directory. By default, this should have been installed at /opt/petagene. Use of this option also requires that the PetaLink library has been preloaded by setting the LD_PRELOAD environment variable. Optionally set the PETASUITE_REFPATH and PGCLOUD_CREDPATH environment variables that are used for data and credentials (default: None)

--keep-tmp

Do not delete the directory storing temporary files after completion.

--license-file LICENSE_FILE

Path to license file license.bin if not in the installation directory.

--no-seccomp-override

Do not override seccomp options for docker (default: None).

--version

View compatible software versions.

--num-gpus NUM_GPUS

Number of GPUs to use for a run. GPUs 0..(NUM_GPUS-1) will be used.

--gpu-devices GPU_DEVICES

GPU devices to use for a run. By default, all GPU devices will be used. To use specific GPU devices, enter a comma-separated list of GPU device numbers. Possible device numbers can be found by examining the output of the nvidia-smi command. For example, using --gpu-devices 0,1 would only use the first two GPUs.